A Bayesian approach to tracking in single molecule fluorescence microscopy

Using fluorescence microscopy with single molecule sensitivity it is now possible to follow the movement of individual fluorophore tagged molecules such as proteins and lipids in the cell membrane with nanometer precision. These experiments are important as they allow many key biological processes on the cell membrane and in the cell, such as transcription, translation and DNA replication, to be studied at new levels of detail. Computerized microscopes generate sequences of images (in the order of tens to hundreds) of the molecules diffusing and one of the challenges is to track these molecules to obtain reliable statistics such as speed distributions, diffusion patterns, intracellular positioning, etc. The data set is challenging because the molecules are tagged with a single or small number of fluorophores, which makes it difficult to distinguish them from the background, the fluorophore bleaches irreversibly over time, the number of tagged molecules are unknown and there is occasional loss of signal from the tagged molecules. All these factors make accurate tracking over long trajectories difficult. Also the experiments are technically difficulty to conduct and thus there is a pressing need to develop better algorithms to extract the maximum information from the data. For this purpose we propose a Bayesian approach and apply our technique to synthetic and a real experimental data set.

Topographical analysis in the SEM using an automatic focusing technique

A novel technique for automated topographical analysis in the SEM has been investigated. It utilizes a 16-bit minicomputer arranged to act as an automatic focusing unit. The computer is coupled to the objective lens of the microscope, by means of a digital to analogue converter, and may regulate the excitation of the lens under program control. Further digital-to-analogue converters allow the computer to act as a programmable scan generator by applying ramp waveforms to the scan amplifiers, permitting the beam to be swept over a small sub-region of the field of interest. The video signal is sampled and applied to an analogue-to-digital converter; the resultant binary numbers are stored in computer memory as an array of values representing relative image intensities within a subregion. A differencing algorithm applied to the collected data allows the level of objective lens excitation to be found at which the sharpness of the image is optimized, and the excitation may be related to the working distance for that subregion through a previous calibration experiment. The sensitivity of the method for detecting small height changes is theoretically of the order of 1 μm.

The inverse problem in magnetic force microscopy--inferring sample magnetization from MFM images.

Nanomagnetic structures have the potential to surpass silicon's scaling limitations both as elements in hybrid CMOS logic and as novel computational elements. Magnetic force microscopy (MFM) offers a convenient characterization technique for use in the design of such nanomagnetic structures. MFM measures the magnetic field and not the sample's magnetization. As such the question of the uniqueness of the relationship between an external magnetic field and a magnetization distribution is a relevant one. To study this problem we present a simple algorithm which searches for magnetization distributions consistent with an external magnetic field and solutions to the micromagnetic equations' qualitative features. The algorithm is not computationally intensive and is found to be effective for our test cases. On the basis of our results we propose a systematic approach for interpreting MFM measurements.

Electrical control of nanoscale functionalization in graphene by the scanning probe technique

Functionalized graphene is a versatile material that has well-known physical and chemical properties depending on functional groups and their coverage. However, selective control of functional groups on the nanoscale is hardly achievable by conventional methods utilizing chemical modifications. We demonstrate electrical control of nanoscale functionalization of graphene with the desired chemical coverage of a selective functional group by atomic force microscopy (AFM) lithography and their full recovery through moderate thermal treatments. Surprisingly, our controlled coverage of functional groups can reach 94.9% for oxygen and 49.0% for hydrogen, respectively, well beyond those achieved by conventional methods. This coverage is almost at the theoretical maximum, which is verified through scanning photoelectron microscope measurements as well as first-principles calculations. We believe that the present method is now ready to realize 'chemical pencil drawing' of atomically defined circuit devices on top of a monolayer of graphene. © 2014 Nature Publishing Group All rights reserved.

Toxicity and imaging of multi-walled carbon nanotubes in human macrophage cells.

Multi-walled carbon nanotubes (MWNTs) have been proposed for use in many applications and concerns about their potential effect on human health have led to the interest in understanding the interactions between MWNTs and human cells. One important technique is the visualisation of the intracellular distribution of MWNTs. We exposed human macrophage cells to unpurified MWNTs and found that a decrease in cell viability was correlated with uptake of MWNTs due to mainly necrosis. Cells treated with purified MWNTs and the main contaminant Fe(2)O(3) itself yielded toxicity only from the nanotubes and not from the Fe(2)O(3). We used 3-D dark-field scanning transmission electron microscopy (DF-STEM) tomography of freeze-dried whole cells as well as confocal and scanning electron microscopy (SEM) to image the cellular uptake and distribution of unpurified MWNTs. We observed that unpurified MWNTs entered the cell both actively and passively frequently inserting through the plasma membrane into the cytoplasm and the nucleus. These suggest that MWNTs may cause incomplete phagocytosis or mechanically pierce through the plasma membrane and result in oxidative stress and cell death.

Scanning gate microscopy of current-annealed single layer graphene

We have used scanning gate microscopy to explore the local conductivity of a current-annealed graphene flake. A map of the local neutrality point (NP) after annealing at low current density exhibits micron-sized inhomogeneities. Broadening of the local e-h transition is also correlated with the inhomogeneity of the NP. Annealing at higher current density reduces the NP inhomogeneity, but we still observe some asymmetry in the e-h conduction. We attribute this to a hole-doped domain close to one of the metal contacts combined with underlying striations in the local NP. © 2010 American Institute of Physics.

Observation of the ordered growth of coronene on Ag(111): a scanning tunnelling microscopy study of vacuum deposited molecules

The molecular ordering of coronene (C24H12) obtained by vacuum-deposition onto predominantly Ag(111) on mica has been investigated using the scanning tunnelling microscope. Real-space topographic images reveal that in certain regions we obtain layer-by-layer ordered growth of the molecules on this substrate which agrees with previous indirect measurements (the growth did not display this ordering in other regions). In our experiments on the ordered regions, we observe the best imaging contrast at a voltage bias of -0.28 V which may correspond to a resonant tunnelling process through the molecules. © 1995.

INFLUENCE OF MICROSTRUCTURE ON THE TOUGHNESS OF CARBON FIBRE/PLASTIC COMPOSITES.

A preliminary study is presented of the relationship between the microstructural aspects of failure and the fracture energy G//1//C for cracking parallel to the fibres in long-fibre/thermoplastic matrix composites. Fracture energies are measured by a new technique, and fracture surfaces generated by the test are examined by scanning electron microscopy.

INFLUENCE OF MICROSTRUCTURE ON THE TOUGHNESS OF CARBON FIBRE/PLASTIC COMPOSITES.

A preliminary study is presented of the relationship between the microstructural aspects of failure and the fracture energy G//l//C for cracking parallel to the fibres in long-fibre/thermoplastic matrix composites. Fracture energies are measured by a new technique, and fracture surfaces generated by the test are examined by scanning electron microscopy.

Scanning transmission electron microscopy investigation of the Si(111)/AlN interface grown by metalorganic vapor phase epitaxy

The structure and chemistry of the interface between a Si(111) substrate and an AlN(0001) thin film grown by metalorganic vapor phase epitaxy have been investigated at a subnanometer scale using high-angle annular dark field imaging and electron energy-loss spectroscopy. 〈1120̄〉AlN ∥ 〈110〉Si and 〈0001〉AlN ∥ 〈111〉 Si epitaxial relations were observed and an Al-face polarity of the AlN thin film was determined. Despite the use of Al deposition on the Si surface prior to the growth, an amorphous interlayer of composition SiNx was identified at the interface. Mechanisms leading to its formation are discussed. © 2010 American Institute of Physics.

Low-temperature (≤600 °C) semi-insulating oxygen-doped silicon films by the PECVD technique for large-area power applications

This work describes the deposition, annealing and characterisation of semi-insulating oxygen-doped silicon films at temperatures compatible with polysilicon circuitry on glass. The semi-insulating layers are deposited by the plasma enhanced chemical vapour deposition technique from silane (SiH4), nitrous oxide (N2O) and helium (He) gas mixtures at a temperature of 350 °C. The as-deposited films are then furnace annealed at 600 °C which is the maximum process temperature. Raman analysis shows the as-deposited and annealed films to be completely amorphous. The most important deposition variable is the N2O SiH4 gas ratio. By varying the N2O SiH4 ratio the conductivity of the annealed films can be accurately controlled, for the first time, down to a minimum of ≈10-7Ω-1cm-1 where they exhibit a T -1 4 temperature dependence indicative of a hopping conduction mechanism. Helium dilution of the reactant gases is shown to improve both film uniformity and reproducibility. A model for the microstructure of these semi-insulating amorphous oxygen-doped silicon films is proposed to explain the observed physical and electrical properties. © 1995.

Low temperature (≤ 600°C) semi-insulating oxygen-doped silicon films by the PECVD technique for large area power applications

This work describes the annealing and characterisation of semi-insulating oxygen-doped silicon films deposited by the Plasma Enhanced Chemical Vapour Deposition (PECVD) technique from silane (SiH4), nitrous oxide (N2O) and helium (He) gas mixtures. The maximum process temperature is chosen to be compatible with large area polycrystalline silicon (poly-Si) circuitry on glass. The most important deposition variable is shown to be the N2O SiH4 gas ratio. Helium dilution results in improved film uniformity and reproducibility. Raman analysis shows the 'as-deposited' and annealed films to be completely amorphous. A model for the microstructure of these Semi-Insulating Amorphous Oxygen-doped Silicon (SIAOS) films is proposed to explain the observed physical and electrical properties. © 1995.

Electron microscopy of polymer-carbon nanotubes composites

Characterization of polymer nanocomposites by electron microscopy has been attempted since last decade. Main drives for this effort were analysis of dispersion and alignment of fillers in the matrix. Sample preparation, imaging modes and irradiation conditions became particularly challenging due to the small dimension of the fillers and also to the mechanical and conductive differences between filler and matrix. To date, no standardized dispersion and alignment process or characterization procedures exist in the trade. Review of current state of the art on characterization of polymer nanocomposites suggests that the most innovative electron and ion beam microscopy has not yet been deployed in this material system. Additionally, recently discovered functionalities of these composites, such as electro and photoactuation are amenable to the investigation of the atomistic phenomena by in situ transmission electron microscopy. The possibility of using innovative thinning techniques is presented. © 2010 Copyright SPIE - The International Society for Optical Engineering.